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Clean up

This commit is contained in:
Arnar Flatberg 2007-02-27 15:05:21 +00:00
parent f73a6db0ee
commit 4de65f1085
1 changed files with 108 additions and 192 deletions
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296
fluents/plots.py
View File

@ -450,15 +450,22 @@ class Plot (View):
View.__init__(self, title) View.__init__(self, title)
logger.log('debug', 'plot %s init' %title) logger.log('debug', 'plot %s init' %title)
self.selection_listener = None self.selection_listener = None
self.fig = Figure()
self.canvas = FigureCanvasGTKAgg(self.fig)
self._toolbar = PlotToolbar(self)
self.canvas.add_events(gtk.gdk.ENTER_NOTIFY_MASK)
self.current_dim = None self.current_dim = None
self._current_selection = None self._current_selection = None
self._background = None
self._frozen = False self._frozen = False
self.use_blit = False self._init_mpl()
def _init_mpl(self):
# init matplotlib related stuff
self._background = None
self._use_blit = False
self.fig = Figure()
self.canvas = FigureCanvasGTKAgg(self.fig)
self.axes = self.fig.gca()
self._toolbar = PlotToolbar(self)
self.canvas.add_events(gtk.gdk.ENTER_NOTIFY_MASK)
self.add(self.canvas)
self.canvas.show()
def set_frozen(self, frozen): def set_frozen(self, frozen):
"""A frozen plot will not be updated when the current """A frozen plot will not be updated when the current
@ -550,26 +557,22 @@ class LineViewPlot(Plot):
-- major_axis : dim_number for line dim (see scipy.ndarray for axis def.) -- major_axis : dim_number for line dim (see scipy.ndarray for axis def.)
-- minor_axis : needs definition only for higher order arrays -- minor_axis : needs definition only for higher order arrays
fixme: slow (cant get linecollection and blit to work) fixme: slow
""" """
def __init__(self, dataset, major_axis=1, minor_axis=None, name="Line view"): def __init__(self, dataset, major_axis=1, minor_axis=None, name="Line view"):
Plot.__init__(self, name)
self.dataset = dataset self.dataset = dataset
self._data = dataset.asarray() self._data = dataset.asarray()
if len(self._data.shape)==2 and not minor_axis: if len(self._data.shape)==2 and not minor_axis:
minor_axis = major_axis - 1 minor_axis = major_axis - 1
self.major_axis = major_axis self.major_axis = major_axis
self.minor_axis = minor_axis self.minor_axis = minor_axis
Plot.__init__(self, name)
self.use_blit = False #fixme: blitting should work
self.current_dim = self.dataset.get_dim_name(major_axis) self.current_dim = self.dataset.get_dim_name(major_axis)
self.line_coll = None
# make axes
self.axes = self.fig.add_subplot(111)
#initial draw #initial draw
x_axis = scipy.arange(self._data.shape[minor_axis]) self.line_coll = None
self.line_segs = [] self.line_segs = []
x_axis = scipy.arange(self._data.shape[minor_axis])
for xi in range(self._data.shape[major_axis]): for xi in range(self._data.shape[major_axis]):
yi = self._data.take([xi], major_axis).ravel() yi = self._data.take([xi], major_axis).ravel()
self.line_segs.append([(xx,yy) for xx,yy in izip(x_axis, yi)]) self.line_segs.append([(xx,yy) for xx,yy in izip(x_axis, yi)])
@ -577,18 +580,10 @@ class LineViewPlot(Plot):
# draw background # draw background
self._set_background(self.axes) self._set_background(self.axes)
# add canvas
self.add(self.canvas)
self.canvas.show()
# add toolbar
self._toolbar = PlotToolbar(self)
# Disable selection modes # Disable selection modes
self._toolbar.freeze_button.set_sensitive(False) self._toolbar.freeze_button.set_sensitive(False)
self._toolbar.set_mode_sensitive('select', False) self._toolbar.set_mode_sensitive('select', False)
self._toolbar.set_mode_sensitive('lassoselect', False) self._toolbar.set_mode_sensitive('lassoselect', False)
#self.canvas.mpl_connect('resize_event', self.clear_background)
def _set_background(self, ax): def _set_background(self, ax):
"""Add three patches representing [min max],[5,95] and [25,75] percentiles, and a line at the median. """Add three patches representing [min max],[5,95] and [25,75] percentiles, and a line at the median.
@ -652,7 +647,7 @@ class LineViewPlot(Plot):
self.axes.add_collection(self.line_coll) self.axes.add_collection(self.line_coll)
#draw #draw
if self.use_blit: if self._use_blit:
if self._background is None: if self._background is None:
self._background = self.canvas.copy_from_bbox(self.axes.bbox) self._background = self.canvas.copy_from_bbox(self.axes.bbox)
self.canvas.restore_region(self._background) self.canvas.restore_region(self._background)
@ -669,20 +664,19 @@ class ScatterMarkerPlot(Plot):
def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, def __init__(self, dataset_1, dataset_2, id_dim, sel_dim,
id_1, id_2, s=6, name="Scatter plot"): id_1, id_2, s=6, name="Scatter plot"):
Plot.__init__(self, name) Plot.__init__(self, name)
self.axes = self.fig.add_subplot(111)
self.axes.axhline(0, color='k', lw=1., zorder=1)
self.axes.axvline(0, color='k', lw=1., zorder=1)
self.current_dim = id_dim self.current_dim = id_dim
self.dataset_1 = dataset_1 self.dataset_1 = dataset_1
self.ms = s self.ms = s
self._selection_line = None
x_index = dataset_1[sel_dim][id_1] x_index = dataset_1[sel_dim][id_1]
y_index = dataset_2[sel_dim][id_2] y_index = dataset_2[sel_dim][id_2]
self.xaxis_data = dataset_1._array[:, x_index] self.xaxis_data = dataset_1._array[:, x_index]
self.yaxis_data = dataset_2._array[:, y_index] self.yaxis_data = dataset_2._array[:, y_index]
# init draw
self._selection_line = None
self.line = self.axes.plot(self.xaxis_data, self.yaxis_data, 'o', markeredgewidth=0, markersize=s) self.line = self.axes.plot(self.xaxis_data, self.yaxis_data, 'o', markeredgewidth=0, markersize=s)
self.add(self.canvas) self.axes.axhline(0, color='k', lw=1., zorder=1)
self.canvas.show() self.axes.axvline(0, color='k', lw=1., zorder=1)
def rectangle_select_callback(self, x1, y1, x2, y2, key): def rectangle_select_callback(self, x1, y1, x2, y2, key):
ydata = self.yaxis_data ydata = self.yaxis_data
@ -726,7 +720,7 @@ class ScatterMarkerPlot(Plot):
markeredgewidth=1.0) markeredgewidth=1.0)
self.axes.add_line(self._selection_line) self.axes.add_line(self._selection_line)
if self.use_blit: if self._use_blit:
if self._background is None: if self._background is None:
self._background = self.canvas.copy_from_bbox(self.axes.bbox) self._background = self.canvas.copy_from_bbox(self.axes.bbox)
self.canvas.restore_region(self._background) self.canvas.restore_region(self._background)
@ -740,11 +734,11 @@ class ScatterMarkerPlot(Plot):
class ScatterPlot(Plot): class ScatterPlot(Plot):
"""The ScatterPlot is slower than scattermarker, but has size option.""" """The ScatterPlot is slower than scattermarker, but has size option."""
def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2, c='b', s=30, sel_dim_2=None, name="Scatter plot"): def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2, c='b', s=30, sel_dim_2=None, name="Scatter plot"):
Plot.__init__(self, name)
self.dataset_1 = dataset_1 self.dataset_1 = dataset_1
self.s = s self.s = s
self.c = c self.c = c
Plot.__init__(self, name)
self.use_blit = False
self.current_dim = id_dim self.current_dim = id_dim
x_index = dataset_1[sel_dim][id_1] x_index = dataset_1[sel_dim][id_1]
@ -754,15 +748,11 @@ class ScatterPlot(Plot):
y_index = dataset_2[sel_dim][id_2] y_index = dataset_2[sel_dim][id_2]
self.xaxis_data = dataset_1._array[:, x_index] self.xaxis_data = dataset_1._array[:, x_index]
self.yaxis_data = dataset_2._array[:, y_index] self.yaxis_data = dataset_2._array[:, y_index]
# labels
self._text_labels = None
# init draw
self.init_draw() self.init_draw()
# add canvas to widget # signals to enable correct use of blit
self.add(self.canvas)
self.canvas.show()
self.connect('zoom-changed', self.onzoom) self.connect('zoom-changed', self.onzoom)
self.connect('pan-changed', self.onpan) self.connect('pan-changed', self.onpan)
self.need_redraw = False self.need_redraw = False
@ -781,7 +771,7 @@ class ScatterPlot(Plot):
self.clean_redraw() self.clean_redraw()
def clean_redraw(self): def clean_redraw(self):
if self.use_blit == True: if self._use_blit == True:
logger.log('notice', 'blit -> clean redraw ') logger.log('notice', 'blit -> clean redraw ')
self.set_current_selection(None) self.set_current_selection(None)
self._background = self.canvas.copy_from_bbox(self.axes.bbox) self._background = self.canvas.copy_from_bbox(self.axes.bbox)
@ -790,7 +780,6 @@ class ScatterPlot(Plot):
self._background = None self._background = None
def init_draw(self): def init_draw(self):
self.axes = self.fig.add_subplot(111)
lw = scipy.zeros(self.xaxis_data.shape) lw = scipy.zeros(self.xaxis_data.shape)
self.sc = self.axes.scatter(self.xaxis_data, self.yaxis_data, self.sc = self.axes.scatter(self.xaxis_data, self.yaxis_data,
s=self.s, c=self.c, linewidth=lw, zorder=3) s=self.s, c=self.c, linewidth=lw, zorder=3)
@ -876,7 +865,7 @@ class ScatterPlot(Plot):
linewidth.put(1, index) linewidth.put(1, index)
self.selection_collection.set_linewidth(linewidth) self.selection_collection.set_linewidth(linewidth)
if self.use_blit and len(index)>0 : if self._use_blit and len(index)>0 :
if self._background is None: if self._background is None:
self._background = self.canvas.copy_from_bbox(self.axes.bbox) self._background = self.canvas.copy_from_bbox(self.axes.bbox)
self.canvas.restore_region(self._background) self.canvas.restore_region(self._background)
@ -888,31 +877,19 @@ class ScatterPlot(Plot):
class ImagePlot(Plot): class ImagePlot(Plot):
def __init__(self, dataset, **kw): def __init__(self, dataset, **kw):
Plot.__init__(self, kw.get('name', 'Image Plot'))
self.dataset = dataset self.dataset = dataset
self.keywords = kw
Plot.__init__(self, kw['name'])
self.axes = self.fig.add_subplot(111)
self.axes.set_xticks([])
self.axes.set_yticks([])
self.axes.grid(False)
# Initial draw # Initial draw
self.axes.imshow(dataset.asarray(), interpolation='nearest', aspect='auto') self.axes.grid(False)
self.axes.imshow(dataset.asarray(), interpolation='nearest')
# Add canvas and show self.axes.axis('tight')
self.add(self.canvas)
self.canvas.show()
# Disable selection modes # Disable selection modes
self._toolbar.freeze_button.set_sensitive(False) self._toolbar.freeze_button.set_sensitive(False)
self._toolbar.set_mode_sensitive('select', False) self._toolbar.set_mode_sensitive('select', False)
self._toolbar.set_mode_sensitive('lassoselect', False) self._toolbar.set_mode_sensitive('lassoselect', False)
def get_toolbar(self):
return self._toolbar
class HistogramPlot(Plot): class HistogramPlot(Plot):
""" Histogram plot. """ Histogram plot.
@ -924,8 +901,6 @@ class HistogramPlot(Plot):
Plot.__init__(self, kw['name']) Plot.__init__(self, kw['name'])
self.dataset = dataset self.dataset = dataset
self._data = dataset.asarray() self._data = dataset.asarray()
self.axes = self.fig.add_subplot(111)
self.axes.grid(False)
# If dataset is 1-dim we may do selections # If dataset is 1-dim we may do selections
if dataset.shape[0]==1: if dataset.shape[0]==1:
@ -933,7 +908,8 @@ class HistogramPlot(Plot):
if dataset.shape[1]==1: if dataset.shape[1]==1:
self.current_dim = dataset.get_dim_name(0) self.current_dim = dataset.get_dim_name(0)
# Initial draw # Initial draw
bins = min(len(self.dataset[self.current_dim]), 20) self.axes.grid(False)
bins = min(self._data.size, 20)
count, lims, self.patches = self.axes.hist(self._data, bins=bins) count, lims, self.patches = self.axes.hist(self._data, bins=bins)
# Add identifiers to the individual patches # Add identifiers to the individual patches
@ -946,9 +922,6 @@ class HistogramPlot(Plot):
bool_ind = scipy.bitwise_and(self._data>=lims[i], bool_ind = scipy.bitwise_and(self._data>=lims[i],
self._data<=end_lim) self._data<=end_lim)
patch.index = scipy.where(bool_ind)[0] patch.index = scipy.where(bool_ind)[0]
# Add canvas and show
self.add(self.canvas)
self.canvas.show()
if self.current_dim==None: if self.current_dim==None:
# Disable selection modes # Disable selection modes
@ -1010,14 +983,13 @@ class BarPlot(Plot):
Ordinary bar plot for (column) vectors. Ordinary bar plot for (column) vectors.
For matrices there is one color for each row. For matrices there is one color for each row.
""" """
def __init__(self, dataset, name): def __init__(self, dataset, **kw):
Plot.__init__(self, kw.get('name', 'Bar Plot'))
self.dataset = dataset self.dataset = dataset
n, m = dataset.shape
Plot.__init__(self, name)
self.axes = self.fig.add_subplot(111)
self.axes.grid(False)
# Initial draw # Initial draw
self.axes.grid(False)
n, m = dataset.shape
if m>1: if m>1:
sm = cm.ScalarMappable() sm = cm.ScalarMappable()
clrs = sm.to_rgba(range(n)) clrs = sm.to_rgba(range(n))
@ -1032,157 +1004,110 @@ class BarPlot(Plot):
left = scipy.arange(1, n, 1) left = scipy.arange(1, n, 1)
self.axes.bar(left, height) self.axes.bar(left, height)
# Add canvas and show
self.add(self.canvas)
self.canvas.show()
# Disable selection modes # Disable selection modes
self._toolbar.freeze_button.set_sensitive(False) self._toolbar.freeze_button.set_sensitive(False)
self._toolbar.set_mode_sensitive('select', False) self._toolbar.set_mode_sensitive('select', False)
self._toolbar.set_mode_sensitive('lassoselect', False) self._toolbar.set_mode_sensitive('lassoselect', False)
def get_toolbar(self):
return self._toolbar
class NetworkPlot(Plot): class NetworkPlot(Plot):
def __init__(self, dataset, **kw): def __init__(self, dataset, pos=None, nodecolor='b', nodesize=40,
# Set member variables and call superclass' constructor prog='neato', with_labels=False, name='Network Plot'):
self.graph = dataset.asnetworkx()
Plot.__init__(self, name)
self.dataset = dataset self.dataset = dataset
self.keywords = kw self.graph = dataset.asnetworkx()
if not kw.has_key('name'): self._prog = prog
kw['name'] = self.dataset.get_name() self._pos = pos
Plot.__init__(self, kw['name']) self._nodesize = nodesize
self._nodecolor = nodecolor
self._with_labels = with_labels
self.current_dim = self.dataset.get_dim_name(0) self.current_dim = self.dataset.get_dim_name(0)
if not kw.has_key('prog'):
kw['prog'] = 'neato'
if not kw.has_key('pos'):
kw['pos'] = networkx.graphviz_layout(self.graph, 'neato')
if not kw.has_key('nodelist'):
kw['nodelist'] = self.dataset.get_identifiers(self.current_dim, sorted=True)
if not kw.has_key('with_labels'):
kw['with_labels'] = True
# Keep node size and color as dicts for fast lookup if not self._pos:
self.node_size = {} self._pos = networkx.graphviz_layout(self.graph, self._prog)
if kw.has_key('node_size') and cbook.iterable(kw['node_size']): self._xy = scipy.asarray([self._pos[node] for node in self.dataset.get_identifiers(self.current_dim, sorted=True)])
kw.remove('node_size') self.xaxis_data = self._xy[:,0]
for id, size in zip(self.dataset[self.current_dim], kw['node_size']): self.yaxis_data = self._xy[:,1]
self.node_size[id] = size
else:
for id in dataset[self.current_dim]:
self.node_size[id] = 30
self.node_color = {} # Initial draw
if kw.has_key('node_color') and cbook.iterable(kw['node_color']): self.default_props = {'nodesize': 50, 'nodecolor':'gray'}
kw.remove('node_color') self.node_collection = None
for id, color in zip(self.dataset[self.current_dim], kw['node_color']): self.edge_collection = None
self.node_color[id] = color self.node_labels = None
else: lw = scipy.zeros(self.xaxis_data.shape)
for id in self.dataset[self.current_dim]: self.node_collection = self.axes.scatter(self.xaxis_data, self.yaxis_data,
self.node_color[id] = 1.0 s=self._nodesize,
c=self._nodecolor,
linewidth=lw,
zorder=3)
# selected nodes is a transparent graph that adjust edge-visibility
# according to the current selection
self.selected_nodes = self.axes.scatter(self.xaxis_data,
self.yaxis_data,
s=self._nodesize,
c=self._nodecolor,
linewidth=lw,
zorder=4,
alpha=0)
self.axes = self.fig.add_subplot(111) self.edge_collection = networkx.draw_networkx_edges(self.graph,
self._pos,
ax=self.axes,
edge_color='gray')
if self._with_labels:
self.node_labels = networkx.draw_networkx_labels(self.graph,
self._pos,
ax=self.axes)
# remove axes, frame and grid
self.axes.set_xticks([]) self.axes.set_xticks([])
self.axes.set_yticks([]) self.axes.set_yticks([])
self.axes.grid(False) self.axes.grid(False)
self.axes.set_frame_on(False) self.axes.set_frame_on(False)
# Add canvas and show
self.add(self.canvas)
self.canvas.show()
# Initial draw
networkx.draw_networkx(self.graph, ax=self.axes, node_size=30, node_color='gray', **kw)
del kw['nodelist']
def get_toolbar(self):
return self._toolbar
def rectangle_select_callback(self, x1, y1, x2, y2, key): def rectangle_select_callback(self, x1, y1, x2, y2, key):
pos = self.keywords['pos'] ydata = self.yaxis_data
ydata = scipy.zeros((len(pos),), 'l') xdata = self.xaxis_data
xdata = scipy.zeros((len(pos),), 'l')
node_ids = []
c = 0
for name,(x,y) in pos.items():
node_ids.append(name)
xdata[c] = x
ydata[c] = y
c+=1
# find indices of selected area # find indices of selected area
if x1 > x2: if x1>x2:
x1, x2 = x2, x1 x1, x2 = x2, x1
if y1 > y2: if y1>y2:
y1, y2 = y2, y1 y1, y2 = y2, y1
assert x1<=x2
assert y1<=y2
index = scipy.nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))[0] index = scipy.nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))[0]
ids = [node_ids[i] for i in index] ids = self.dataset.get_identifiers(self.current_dim, index)
ids = self.update_selection(ids, key) ids = self.update_selection(ids, key)
self.selection_listener(self.current_dim, ids) self.selection_listener(self.current_dim, ids)
def lasso_select_callback(self, verts, key=None): def lasso_select_callback(self, verts, key=None):
pos = self.keywords['pos'] xys = scipy.c_[self.xaxis_data[:,scipy.newaxis], self.yaxis_data[:,scipy.newaxis]]
xys = []
node_ids = []
c = 0
for name,(x,y) in pos.items():
node_ids.append(name)
xys.append((x,y))
c+=1
index = scipy.nonzero(points_inside_poly(xys, verts))[0] index = scipy.nonzero(points_inside_poly(xys, verts))[0]
ids = [node_ids[i] for i in index] ids = self.dataset.get_identifiers(self.current_dim, index)
ids = self.update_selection(ids, key) ids = self.update_selection(ids, key)
self.selection_listener(self.current_dim, ids) self.selection_listener(self.current_dim, ids)
def set_current_selection(self, selection): def set_current_selection(self, selection):
ids = selection[self.current_dim] # current identifiers linewidth = scipy.zeros(self.xaxis_data.shape, 'f')
node_set = set(self.graph.nodes()) index = self.get_index_from_selection(self.dataset, selection)
if len(index) > 0:
selected_nodes = list(ids.intersection(node_set)) linewidth.put(2, index)
unselected_nodes = list(node_set.difference(ids)) nodelist = selection[self.current_dim]
selected_edges = self.grap
if self.node_color: self.selected_nodes.set_linewidth(linewidth)
unselected_colors = [self.node_color[x] for x in unselected_nodes]
else:
unselected_colors = 'gray'
if self.node_size:
unselected_sizes = [self.node_size[x] for x in unselected_nodes]
selected_sizes = [self.node_size[x] for x in selected_nodes]
else:
unselected_sizes = 30
selected_sizes = 30
self.axes.collections = []
networkx.draw_networkx_edges(self.graph,
edge_list=self.graph.edges(),
ax=self.axes,
**self.keywords)
networkx.draw_networkx_labels(self.graph, **self.keywords)
if unselected_nodes:
networkx.draw_networkx_nodes(self.graph, nodelist=unselected_nodes, \
node_color='gray', node_size=unselected_sizes, ax=self.axes, **self.keywords)
if selected_nodes:
networkx.draw_networkx_nodes(self.graph, nodelist=selected_nodes, \
node_color='r', node_size=selected_sizes, ax=self.axes, **self.keywords)
self.axes.collections[-1].set_zorder(3)
self.canvas.draw() self.canvas.draw()
class VennPlot(Plot): class VennPlot(Plot):
def __init__(self, name="Venn diagram"): def __init__(self, name="Venn diagram"):
Plot.__init__(self, name) Plot.__init__(self, name)
self.axes = self.fig.add_subplot(111)
self.axes.grid(0)
self._init_bck() self._init_bck()
# init draw
for c in self._venn_patches: for c in self._venn_patches:
self.axes.add_patch(c) self.axes.add_patch(c)
for mrk in self._markers: for mrk in self._markers:
@ -1192,14 +1117,10 @@ class VennPlot(Plot):
self._last_active = set() self._last_active = set()
self.axes.set_xticks([]) self.axes.set_xticks([])
self.axes.set_yticks([]) self.axes.set_yticks([])
self.axes.grid(0)
self.axes.axis('equal') self.axes.axis('equal')
self.axes.grid(False)
self.axes.set_frame_on(False) self.axes.set_frame_on(False)
# add canvas to widget
self.add(self.canvas)
self.canvas.show()
def _init_bck(self): def _init_bck(self):
res = 50 res = 50
a = .5 a = .5
@ -1293,11 +1214,6 @@ class VennPlot(Plot):
self.axes.figure.canvas.draw() self.axes.figure.canvas.draw()
def rectangle_select_callback(self, x1, y1, x2, y2, key): def rectangle_select_callback(self, x1, y1, x2, y2, key):
"""event1 and event2 are the press and release events"""
#x1, y1 = event1.xdata, event1.ydata
#x2, y2 = event2.xdata, event2.ydata
#key = event1.key
verts = [(x1, y1), (x2, y2)] verts = [(x1, y1), (x2, y2)]
if key!='shift': if key!='shift':
for m in self._markers: for m in self._markers: